Align Phosphoribosyl isomerase A; 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase; EC 5.3.1.16; N-(5'-phosphoribosyl)anthranilate isomerase; PRAI; EC 5.3.1.24; Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (uncharacterized)
to candidate BWI76_RS18945 BWI76_RS18945 1-(5-phosphoribosyl)-5-((5- phosphoribosylamino)methylideneamino)imidazole-4- carboxamide isomerase
Query= curated2:P60583 (243 letters) >FitnessBrowser__Koxy:BWI76_RS18945 Length = 245 Score = 135 bits (341), Expect = 6e-37 Identities = 87/244 (35%), Positives = 137/244 (56%), Gaps = 13/244 (5%) Query: 3 ILLPAVDVVDGRAVRLVQGKAGSETEYGS-ALDAALGWQRDGAEWIHLVDLDAAFGRGSN 61 +++PA+D++DG VRL QG G + +YG+ L + GAE +HLVDL A Sbjct: 1 MIIPALDLIDGTVVRLHQGDYGQQRDYGNDPLPRLQSYAAQGAEVLHLVDLTGAKDPAKR 60 Query: 62 R-ELLAEVVGKLDVRVELSGGIRDDDSLAAALATGCARVNLGTAALENPQ----WCARAI 116 + LL ++V ++V V++ GG+R + +AA L G ARV +G+ A+++P+ W R Sbjct: 61 QIPLLKKLVAGVNVPVQVGGGVRTEQDVAALLEAGVARVVVGSTAVKSPEVVKGWFKRFG 120 Query: 117 GEHGDKVAVGLDVQI-IDGQHRLRGRGW-ETDGGDLWEVLERLERQGCSRYVVTDVTKDG 174 +H + + LDV+I +G+ ++ GW E G L E++E + G + TD+++DG Sbjct: 121 PQH---LVLALDVRIDAEGRKQVAVSGWQENSGVTLEELVESYQSVGLQHVLCTDISRDG 177 Query: 175 TLGGPNLDLLGAVADRTDAPVIASGGVSSLDDLRAIATLTGRGVEGAIVGKALYAGRFTL 234 TL G N+ L V R P +A + DL IA L G GV G IVG+AL G+F + Sbjct: 178 TLAGSNVSLYEEVCAR--YPQVAFQSSGGIGDLNDIAALLGTGVRGVIVGRALLEGKFNV 235 Query: 235 PQAL 238 +A+ Sbjct: 236 TEAI 239 Lambda K H 0.318 0.138 0.407 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 197 Number of extensions: 11 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 243 Length of database: 245 Length adjustment: 24 Effective length of query: 219 Effective length of database: 221 Effective search space: 48399 Effective search space used: 48399 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory